1) Research interests

Understand what are the drivers of genome size variation:

Funded by ANR https://anr.fr/Projet-ANR-20-CE02-0008

Animals display strikingly complex and variable genome architectures. For example, genome size and genome content vary tremendously between animals. More than two orders of magnitude separate the 100 million base pair (bp) genome of Caenorhabditis elegans from the 32 billion bp of the Mexican axolotl (Ambystoma mexicanum). This variation is, however, not explained by a variation in the number of protein-coding genes. Indeed, our genome is 20 times larger than the one of the Drosophila fruit fly even if we have only 1.5 times more protein-coding genes1 . As a general pattern, genome size is positively correlated to the proportion of non-coding DNA and repeated sequences (especially transposable elements, TEs) but not to the number of genes. In the 2000s, Michael Lynch published a series of influential studies postulating that many aspects of genome architecture complexity have evolved mainly through the action of non-adaptive forces such as genetic drift and mutation2 . Lynch and Conery3 observed that genome size is negatively correlated with the level of neutral polymorphism (which is proportional to the product of effective population size, Ne, and mutation rate, µ). They concluded that the proliferation of transposable elements and non-coding DNA is responsible for mildly deleterious mutations that could not be counter-selected in organisms with low genetic diversity, leading to an increase in genome size in these species. 

Although appealing because it is based on universal principles of population genetics, Lynch's theory (also known as the mutational-hazard hypothesis, MH) has rarely been tested empirically. In the PhD project, we propose an alternative strategy to test Lynch’s theory, namely to specifically analyze animal groups that have undergone repeated Ne decreases. Indeed, a comparison between closely related species with different long-term Ne is critical to demonstrate the importance of genetic drift on the evolution of genome architecture. Five biological models will be used, including Asellidae isopods (Lefébure et al., 2017), passerine birds (Leroy et al., 2021), Drosophila (Sessegolo et al., 2016), swallowtail butterflies (Allio et al., 2019) and ants, along with an in silico model (Beslon et al., 2010). This project aims are :

 ● Generate genomic resources for these groups : genome assembly combining Minion long-reads (long but costly and error-prone) and Illumina short-reads (short by cheap and accurate) technologies. ● Transposable element (TE) annotation for the reference genomes ● Estimation of polymorphism pattern of SNP and TE ● Assessment of the impact of TEs on genome size ● Effective population size (Ne) estimation ● Assessing the fitness of TE dynamics using polymorphism data ● Historical Ne reconstruction based on interspecific divergence/rate of evolution using a Bayesian method developed by a member of the project The main goal of the phD project will be to evaluate the influence of Ne (and other relevant parameters such as the recombination and indel rates) on the evolution of genome size and proportion of non-coding DNA as well as the associated dynamics of TE

BirdIslandGenomic project

Oceanic islands provide great opportunities for studying biological evolution. In this project, we propose to investigate island evolution from the genomic point-of-view. Understanding the influence of population size variation on molecular evolution is currently a major topic in the field. Since island species have evolved in isolated and small populations, they provide an unique opportunity to study the impact of non-adaptive forces on biological evolution.

Thibault Leroy, Marjolaine Rousselle, Marie-Ka Tilak, Aude Caizergues, Céline Scornavacca, Maria Recuerda Carrasco, Jérôme Fuchs, Juan Carlos Illera, Dawie H. De Swardt, Christophe Thébaud, Borja Milà, Benoit Nabholz. Endemic island songbirds as windows into evolution in small effective population sizes. https://www.biorxiv.org/content/10.1101/2020.04.07.030155v1

Publications :

• M. Gabrielli, B. Nabholz, T. Leroy, B. Milá and C. Thébaud, 2020. Within-island diversification in a passerine bird. Proceedings of the Royal Society B: Biological Sciences. 287: 20192999. 

• Leroy T, Anselmetti A, Tilak MK, Bérard S, Csukonyi L, Gabrielli M, Scornavacca C, Milá B, Thébaud C and Nabholz B. A bird’s white-eye view on neo-sex chromosome evolution. 2019. bioRxiv 505610, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. DOI: 10.1101/505610. [Datasets and scripts]

Understanding the link between life-history traits variation and molecular evolution

I would like to understand how, and to which extend, a series of life-history traits, such as longevity, body-mass, generation time, "life style" and reproduction system, influence molecular evolution. When they vary, these traits are expected to have an impact on several evolutionary forces (i.e., mutation, drift, recombination) which in turn will influence genomes evolution.

Large species have the tendency to live longer and reach sexual maturity older than small species. Therefore large species are expected to have longer generation time and should show reduced substitution rate compared to smaller species. If this relationship seem to work for mammals, it is still debated for birds (where molecular clock is still largely used). Similarly, large animals are also expected to have, on average, smaller population size than small animals. Because population size affect genetic drift, large animals should not be able to eliminate slightly deleterious mutation as efficiently as small animals. Using large datasets of mitochondrial and nuclear loci, I'm testing the above expectation regarding the effect of body size on efficiency of selection and substitution rate variation in birds and mammals.

Phylogeny of Papilionidae and genomic adaptation to host plant

This project is leaded by Fabien Condamine. We study the phylogeny of Swallowtail butterflies (Lepidoptera: Papilionidae) using mitogenomes and full genomes sequences. Marianne Annonier has just started a PhD project on the subject (2018-2021). The project ERC GAIA : "A Genomic and Macroevolutionary Approach to Studying Diversification in an Insect Plant Arms Race" have been funded for 5 years (2020-2025) : see news

Former Project (could be resurrected some days?)

Influence of base composition on phylogenetic reconstruction

I have a general interesting in phylogenetic and molecular dating methods. Currently, I focus on the influence of base composition variation on phylogenetic reconstruction. I'm particularly interested in the birds phylogeny where the basal relationships among Neoaves (composed of all the living birds except Ratites and Galloanserae) is still unresolved.

The genomic footprints of domestication

I'm part of the large ARCAD project where I focus on the comparative population genomic project.